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OpenMM testbed for constant-pH methodologies.
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choderalab/protons
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Testbed for constant-pH methodologies using OpenMM.
protons/ - Python module implementing constant-pH methodologies in Python
calibration.py - Calibration engines cnstphgbforces.py - CustomGBForces that exclude contributions from discharged protons ligutils.py - Work in progress code for ligand parametrization. tests/ - Unit testsprotons/examples/
explicit-solvent-example.py - explicit solvent NCMC example amber-example/ - example system set up with AmberTools constant-pH tools calibration-implicit/ - terminally-blocked amino acids parameterized for implicit solvent relative free energy calculations calibration-explicit/ - terminally-blocked amino acids parameterized for explicit solvent relative free energy calculationsreferences/ - some relevant literature references
protons will eventually be made conda installable. The list of dependencies can be foundhere.
- Bas Rustenburgbas.rustenburg@choderalab.org
- Gregory Rossgregory.ross@choderalab.org
- John D. Choderachoderaj@mskcc.org
- Patrick Grinawaygrinawap@mskcc.org
- Jason Swailsjason.swails@gmail.com
- Jason Wagonerjawagoner@gmail.com
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OpenMM testbed for constant-pH methodologies.
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